Asian elephant (Elephas maximus) plays a significant role in natural ecosystems and it is considered as an endangered animal. Molecular genetics studies on elephants’ dates back to 1990s. Microsatellite markers have been the preferred choice and have played a major role in ecological, evolutionary and conservation research on elephants over the past 20 years. However, technical constraints especially related to the specificity of traditionally developed microsatellite markers have brought to question their application, specifically when degraded samples are utilized for analysis. Therefore, we analyzed the specificity of 24 sets of microsatellite markers frequently used for elephant molecular work. Comparative wet lab analysis was done with blood and dung DNA in parallel with in silico work. Our data suggest cross-amplification of unspecific products when field-collected dung samples are utilized in assays. The necessity of Asian elephant specific set of microsatellites and or better molecular techniques are highlighted.
Elephas maximus maximus Linnaeus, the Sri Lankan subspecies is the largest and the darkest among Asian elephants. Patches of depigmented areas with no skin color on the ears, face, trunk, and belly morphologically differentiate it from the others. The elephant population in Sri Lanka is now limited to smaller areas and protected under Sri Lankan law. Despite its ecological and evolutionary importance, the relationship between Sri Lankan elephants and their phylogenetic position among Asian elephants remains controversial. While identifying genetic diversity is the key to any conservation and management strategies, limited data is currently available. To address such issues, we analyzed 24 elephants with known parental lineages with high throughput ddRAD-seq. The mitogenome suggested the coalescence time of the Sri Lankan elephant at ~0.2 million years, and sister to Myanmar elephants supporting the hypothesis of the movement of elephants in Eurasia. The ddRAD-seq approach identified 50,490 genome-wide SNPs among Sri Lankan elephants. The genetic diversity within Sri Lankan elephants assessed with identified SNPs suggests a geographical differentiation resulting in three main clusters; north-eastern, mid-latitude, and southern regions. Interestingly, though it was believed that elephants from the Sinharaja rainforest are of an isolated population, the ddRAD-based genetic analysis clustered it with the north-eastern elephants. The effect of habitat fragmentation on genetic diversity could be further assessed with more samples with specific SNPs identified in the current study.
The genus Cinnamomum of the family Lauraceae is an economically important crop. The Ceylon cinnamon (Cinnamomum verum syn. C. zeylanicum) has an exceptional position in the global cinnamon market. In addition to the cultivated species, Sri Lanka is home to seven endemic wild Cinnamomum species, C. capparu-coronde, C. citriodorum, C.
The Sri Lankan Leopard ( Panthera pardus kotiya ) is an endangered subspecies restricted to isolated and fragmented populations in Sri Lanka. Among them, the melanistic leopards have been recorded on rare occasions. The existing literature suggests that melanism evolved several times in the Felidae family, with three separate species revealing distinct mutations. Nevertheless, the mutations in the remaining species, including Sri Lankan black leopard, are unknown. We used reference-based assembled the nuclear genomes of Sri Lankan normal and black leopard and de novo assembled mitogenomes of the same to investigate the genetic basis, adaptive significance, and evolutionary history of the Sri Lankan black leopard. Our data suggested coalescence time of Sri Lankan regular and black leopards at ~0.5 Million years, sisters to Panthera pardus lineage. Interestingly, in the black leopard, a single nucleotide polymorphism in exon-4 possibly completely ablates Agouti Signaling Protein (ASIP) function. Existing genomic data suggest new a species-specific mutation of the ASIP gene in the Felidae family, contributing to naturally occurring colouration polymorphism. As such, the Sri Lankan black leopard and normal leopard probably evolved from the same ancestor, while the mutation in the ASIP gene resulted in black coat colour. This rare mutation could be adaptable to the environment that back leopards reported, camouflage, with a likelihood of recurrence and transmission to future generations. However, protecting this sensitive environment is critical for the conservation of the existing populations and providing breeding grounds.
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